therealchrisneale

I have the same issue with Gromacs 2019.6 patched with plumed 2.7.2. without the -plumed flag, gmx mdrun works fine. With that flag: $ gmx mdrun -s PLUMED.tpr -rerun PLUMED.gro...

Also, I just verified gromacs 2020.6 patched with plumed 2.7.2 has the same problem. It's related to -rerun with -plumed. I'm guessing it's because the viral and pressure terms are...

In case it is useful, here's results for the test posted in this thread from v2.2.4 + cray + A100 + nvidia kernel 510.85.02 + cudatoolkit 11.7.0 + charliecloud in...

Not perfect, but perhaps the best available option: ``` import warnings with warnings.catch_warnings(): warnings.simplefilter("ignore") traj = mdtraj.load('my.gro') ```

Not sure how helpful this will be, but here is what I get for a successful build with LigParGen v2.1 (even with that strange smiles string for phenol): $ LigParGen...

CC#N works in the command line version. Here is the output I got for the gromacs .itp file and the .pdb file: ########################## $ cat CC#N.itp ; Writted by Leela...

This one works for something close that is neutral (I realize it’s not exactly what you want) FC(F)(F)S(=O)(=O)NS(=O)(=O)C(F)(F)F

Your PDB file is incorrect due to spacing issues. Some noted below, but also the entire PDB format depends on certain columns so you might get better results if you...

``` $ conda env create -f environment.yml -n septop --solver=libmamba ... $ conda list -n septop # packages in environment at /Users/chrisneale/opt/anaconda3/envs/septop: # # Name Version Build Channel ambertools 24.8...

For the second error, I can reproduce by simply trying to read the hybrid top file that was generated earlier in the script. ``` import parmed as pmd gro =...